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Calculate Niche Differential Expression Genes

Source: R/SingleSampAnalysis.R
CalSampDEGs.Rd

Identifies differentially expressed genes between niche and bystander cells, both globally and per cell type. Generates volcano plots and faceted volcano plots for visualization.

Usage

CalSampDEGs(
  STID_obj = NULL,
  samp_mode = "SS",
  loop_id = "LoopAllSamp",
  samp_grp_index = FALSE,
  meta_key = NULL,
  niche_key = NULL,
  group_by = NULL,
  group_value = NULL,
  assay_id = "Spatial",
  test_method = "wilcox",
  logfc_thres = 1,
  min_pct = 0.01,
  padj_thres = 0.05,
  adjust_method = "BH",
  topGeneN = 5,
  remove_genes = NULL,
  col = COLOR_LIST[["PALETTE_WHITE_BG"]],
  return_data = TRUE,
  grp_nm = NULL,
  dir_nm = "M3_CalSampDEGs",
  ...
)

Arguments

STID_obj

An STID object containing niche analysis results

samp_mode

Character, sample type - "SS" (single sample) or "MS" (multi-sample) (default: "SS")

loop_id

Character, sample grouping identifier (default: "LoopAllSamp")

samp_grp_index

Logical, whether to group by sample groups in MS mode (default: FALSE)

meta_key

Character, metadata key for MS mode when niche_key is NULL

niche_key

Character, niche key to analyze

group_by

Character, column name for cell type grouping

group_value

Character vector, specific cell types to analyze

assay_id

Character, assay name (default: "Spatial")

test_method

Character, statistical test to use (default: "wilcox")

logfc_thres

Numeric, log2 fold change threshold (default: 1)

min_pct

Numeric, minimum percentage of cells expressing gene (default: 0.01)

padj_thres

Numeric, adjusted p-value threshold (default: 0.05)

adjust_method

Character, p-value adjustment method (default: "BH")

topGeneN

Integer, number of top genes to label (default: 3)

remove_genes

Character vector, genes to exclude from analysis

col

Color palette for visualization (default: COLOR_LIST$PALETTE_WHITE_BG)

return_data

Logical, whether to return results list (default: TRUE)

grp_nm

Character, group name for output organization (default: NULL)

dir_nm

Character, directory name for output (default: "M3_CalSampDEGs")

...

Additional parameters for FindAllMarkers and FindMarkers functions

Value

If return_data = TRUE, returns a list of DEG results per sample

Examples

if (FALSE) { # \dontrun{
# Find DEGs between niche and bystander cells
results <- CalSampDEGs(
  STID_obj = STID_obj,
  niche_key = "niche_virulence",
  group_by = "cell_type",
  logfc_thres = 0.5,
  padj_thres = 0.05,
  topGeneN = 5
)
} # }